Not here, Not there, Somewhere else, Very different !

I borrowed these lines from Rabindranath Tagore, and these lines are spinning in my head for past few days, lines are in Bangla, but I translated them with my funny English! Okay, the whole things abou making goals, for the next days on this blog!

I came to this morose world with a unnecessary curious mind..I asked so much questions that bothered everyone around me. Now I am grown up, cant do the same..but whenever today I see lines of freezers in the lab, I think of a horror film, where zombies would peep out anytime! Today, I must think freezers as freezers, not zombieland! And thats the reason why this blog is! For my dual mind, where freezers are freezers, and where they are bunch of mysteries!

And also for those, who disgustingly ask, “what is hobby?” “I write” “What you write?” “daydreams!” !! No, to answer, “I write under cover of RAINRHYME.WORDPRESS! here’s the link moron!!”

Then, where the goals come from? When I make plans, they are failed, when I don’t they are awesome! yes, procrastination it is, but thats the happiness also 🙂 So, when I like I’ll write, when I don’t, I won’t! And all of my friends (NO FOLLOWER!) definitely would understand this.

I am not that angel-like actually, I love when people read my stuffs, like them…But I am tired this days sometimes. When I followed a few friends, my reader section was clean, I read all of their writings, but now, what I would read, and what not?? At this point comes the pain of making posts more attractive, more eye-catching…I want to remind all of my friend’s names, what they write about..But is it possible really if I have twenty thousands five hundreds and forty two followers??

So, my goal on this first day is, trying to write continuously, get to know my friends, read a lot of science stuffs and again, write!! 😀 😀

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Holy Cross, we shall be TRUE !

In response to The Daily Post’s writing prompt: “Teacher’s Pet.”

When I am asked to tell about my school-college-university journey, I feel somehow awkward..  somedays earlier, one of my colleagues said, you studied in 4 schools in your 10 years primary and secondary life? then, you couldn’t have a soul-friend!

Ya, she’s right! I studied at a kindergarten for two years in Chittagong, another city. All I could remember, loud rhymes, beautiful class teacher and lots of weird activities 🙂

Then moved to Dhaka and was admitted in  a government school. Here, the school compound was huge, and I met many friends from lower or lower-middle class society..We managed to make adventures in the horrified corners, trees, and as usual a ghost in the washroom! 😀 But as I said, class, here I learned how to love people whatever they are! Life is the best teacher though…

Then another school, one of the top and aristocrat girls school in Dhaka.. It was suffocating! grade six, when a girl needs care and mental shelter most, I learned what upper social class is!!

And finally, came to my HOLY CROSS, at grade 8, and the journey ended at grade 12. But did it end? Never! Holy Cross taught me whatever your class, religion, race, complexion etc etc etc is, you are lovable and respectable, and you must give the reward back! Try to do a single thing for another, littlest it be!

Featured image

My teachers, Sister Philomina Quiya, Sharmin miss, Jharna Mitra miss, Mrs Fahima Gias, Rezwana miss, Chandraboti miss, Pinaru sir, Ostadji (islam religion teacher), Sharkar sir, Mrs Sattar…how many names are peeping on my mind! The wonderful ladies were the living examples of what a LADY is! They were confident, erudite,  independent and affectionate!

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The most amazing lady of my life, Sister Joseph Mary! This wonderful lady came to our land, from another part of the world, and the whole life, lived and loved us all! When I found her, she was a very very old lady, but strongest than all! I can remember yet, how she used to walk on her shaky old legs, her normal skirt, flat shoes, climbing stairs, and finally teaching us English accent, in her own artful style!

Once she burst out crying and scolded us loud when she saw a girl sitting on the new building wall..We were bored to see a old lady crying! But when she told us, we were mum. One of her close friends died this way, that day I realized, preachers are human too! They cry out for their own family, whether its long forsaken, or whether its the new us! Next day, she started working on making safety grills on the walls! gratitude is so small for this extraordinary lady!

I wouldn’t lengthen my post anymore, just would song that we sang everyday..

“Hail to thee, our Alma Mater,
We, with loving hearts, proclaim.
Long may our college live,
Ever glorious be her name.
Orient skies smile upon us,
As we pledge our love anew,
Holy Cross, we shall be loyal,
Holy Cross we shall be true.
Through the years our song will echo
As we walk our paths apart.
Each note will bind us closely
To our Alma Mater’s heart”

Letter to Blogging 101

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Dear Blogging 101,

Today is 31 January, my last day with you and so my first letter. Who reminds someone when she’s with that person? This letter is not just a gratitude but a intimate picture of bonding and sharing during this course!

I started my blog journey, on January 01, with the name RAINRHYME, a new avatar in this vast internet, with the blog, Lets start it! (later named Dreaming in a dream). There was none in my reader except, the daily post. Then came the name Blogging University! A University on blogging?? took a course, Blogging 101, and boom!

The entire month, I paid heed to my lectures, sometimes could run fast, sometimes couldn’t. But for a beginner like me, it was wow!  I found answers, should I blog? should I write on both personal and science stuffs? And the commons was always there 🙂

I never read scientific journals so eagerly as I do now for posting some biology stuffs (though none read them I guess 🙂 ). I found so much fun reading and writing about Metagenomic virus detection from clinical samples that it changed my ambition from Cell Biology PhD to Molecular Biology! I have known my interests, myself while writing!

I wanted to find some friends, who would KNOW ME, without previous KNOWING ME. So, I changed my sharing pattern, and its no social media here ! Yes, my follower number is less, but who bothers?? I don’t even call them followers, they are my friends! from all over the world! I have known some excellent personalities here! So strong, so nice they are! And some labmates too 🙂 Once a thought came to my mind, should I attach this big size photo of me on my home page? Isn’t it looking chick-flick? Then I thought about the people here, felt them so close, so why not sharing my show-case with them?

The letter is too big already, but it is my last letter to you 101, so I’d tell everything I felt! The person I should thank most, Michelle W. Thank you mam! 😀 I loved your word “weekend warriors” most!

You know, what the great thing is? It is GOOD, but not a BYE yet! I have registered for the Blogging 201 course 😀 Hope to see you all in the magical paths of readers, daily prompts, photo event, writing event and all! Hope to jump on a high five whenever we meet! “Arreeh! aren’t you from the Blogging 101 course? How are you doing mate!” 😀

Hope to meet you soon!

Yours, Sadia 🙂

The quintupled hymn

I was searching for the right word, to picturize the beautiful call for prayer, five times a day, the Adhan. Islam has already become the religion of debates, of fear these days, and I am not going to this path anyway. To me, the evening bells from mandir (hindu temple), the evening bells from church, or the evening adhan from mosque, all are equally respectful! But as a muslim, Adhan not only reminds me of prayer, but also reminds me the first days of Islam, when all were equal, the honor of first muazzin or adhan reciter was given to Hazrat Bilal(RA), a slave! And what have we made ourselves today! We have made even different Adhans for different muslim groups!

It is said that, Dhaka is a city of mosques. We have thousands of mosques in neighborhoods, main roads, everywhere. Five times a day muazzins recite its beautiful rhythms, “Allah is greatest, I bear witness there is no God but Allah, I bear witness Muhammad is the messenger of Allah, Hasten to worship, hasten to success!” I love the beautiful part of the Fazr (early morning) salat, “prayer is better than sleep”..I am very lazy person, I cant wake up that time most of the days, but whenever this only line is recited I can’t sleep anymore!

One day, one of my friends called from Australia. Adhan (we call it Azan) was being recited, as always, on loudspeaker, my friend said, turn your voice down, how long I haven’t heard it! Yea, thats a sound pollution of course, when its started at thousands of mosques at a time, in this super duper noisy city, but is it really? No! as I repeatedly tell about the religious culture of our nation, its another example of it. Our non-muslim friends, regard Adhan as clocks! As the way, clocks in churches, in our country, when Adhan for Zuhr prayer is called, its 1 PM! simple!

Days become long, days become short, whole year round, we understand this by the changes in Adhan times. Children goes to field when its afternoon, when Aasr adhan is calling, come back home when its dusk, Magrib adhan. Don’t come home after magrib! moms from all religion, same language! When the sun is setting, first the Magrib adhan, completed, then the bells from hindu homes..no clashes at all! Thus in this peaceful country of rains, this hymn, simple, no instruments, only bare voice, only some lines, quintupled, reminds us of prayer, of that unity we have forgot in this mundane world!

Ancient “genomic parasites” spurred evolution of pregnancy in mammals

Science Life

Studies of Embryos by Leonardo da Vinci Studies of Embryos by Leonardo da Vinci

The evolution of biological structures and functions from existing ones, for example a forearm from a fish fin, has been studied for centuries. But how do entirely new things evolve? It’s a tricky question to answer, but Vincent Lynch, PhD, assistant professor of human genetics at the University of Chicago, and his colleagues shed some light on this process in a new study published online today in Cell Reports.

Taking a look at the origins of pregnancy in mammals, they identified large-scale genetic changes that marked the transition from egg laying to live birth. The researchers found thousands of genes that evolved to be turned on or off in the uterus in early mammals, including many with critical functions in establishing maternal-fetal communication and suppressing the mother’s immune system so that a fetus is not attacked. What was most surprising, however, was what…

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6 Tips for a successful ELISA

Being bio-reactive

ELISA are immunoassays widely used in biomarker detection and validation. They have been used in research and clinical settings for more than 40 years, and they allow to quantify, in a simple way, thousands of biomarkers. New ELISAs are being developed every day, either for new biomarkers or new species. They can also be used to detect contaminants in food, water or industrial processes.Raybiotech ELISA Kits by tebu-bio

Technology-wise, there are several types of ELISAs, depending on whether they are based on double (or sandwich) antibody detection, direct detection, competitive detection, etc. It is not the scope of this post to enter into details about the different formats that an ELISA can have, but if you think that you need this info, feel free to suggest that I do a post on that!

Nevertheless, the aim of this post is to give some hints on how to reach the best result for your ELISA…

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Good News for Clinical Laboratory Scientists: iPad App For Medical Laboratory Pipetting Protects Lives and Jobs! Read more: Good News for Clinical Laboratory Scientists: iPad App For Medical Laboratory Pipetting Protects Lives and Jobs!

just wow 😀 😀

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Dark Daily Donna Marie Pocius 23 January 2015

Scientists at the prestigious Cambridge, Massachusetts-based Whitehead Institute for Biomedical Research at the Massachusetts Institute of Technology recently unveiled the iPipet system. This in an innovative system which employs tablet computers such as iPads to guide the tedious and often dangerous task of manual pipetting.

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A journey to the Swan Lake

In response to The Daily Post’s writing prompt: “Once Upon a Time.”

Listen my little kitties, listen to your granny..It was a sunny, yes, very sunny winter day..I might be old today, but the day, I still can remember it. It was the day of January, 25, 2015. The date of today. No, no, don’t think I am making up the date..It really was 25 January, your granny’s not that old yet!

It was the day of “Saraswati puja“. Nowdays, you just don’t bother about old religious programs, but once they were great festivals. People from all religions, muslims, hindus, buddhists, christians, all gathered in the puja field..Goddess Saraswati, the goddess of knowledge, with her four hands (mind, sense; intellect, reasoning; imagination, creativity; self consciousness, ego), her book of knowledge, her crystal garland of inner reflection, her water of purity and her musical instrument of all creative arts and sciences; called all her pupils… And above all, mother’s SWAN, not a normal one, her beautiful, enormous, snow-white swan..You know, why swan is her vehicle? because, you give her swan mixture of water and milk, it would able to drink the milk alone…Knowledge is not only learning, but the ability to differ good and bad!

Goddess Saraswati statue by Deparment of fine arts, Dhaka University photo courtesy: http://news.priyo.com/photo/2011/feb/09/19373.html, https://www.flickr.com/photos/arrajib/8557738043/?rb=1

I know, what you are thinking bunnies, that, I am a muslim, pray five times a day, don’t believe in Gods and Goddesses, wouldn’t take a mark of sindur or chandan on my forhead, then what was my relation with the veneration, isn’t it? Yes, you are right. On that day, people also asked that. But it was our country of harmony, that’s a rare word today.

Our University of Dhaka organized a big big big festival that day, actually for many years. All the departments, from science faculty, arts, business studies..54 departments established saraswati statue, in their own way, reflecting the theme of their department..You know, there was a statue from Islamic Studies department as well! Huh, what harmonious days they were!

But if the day was that easy, may be I wouldn’t tell you this story. The huge monsters of politics swallowed the whole country..No security, nothing, anytime you might be burnt in the petrol bomb! Boom! and you would be a lump of flesh! But dear, should we let the evil win! No, we couldn’t! We decided to visit mother saraswati, might we didn’t believe her, but we believed the power of knowledge, good and bad!

After office, I came out, whole monthly salary in handbag, lots of cash in a day of chaos outside. No, I didn’t have a horse, a white one as you see in fairy tales, but I made myself entered in a crowded bus..Our university was not far, but there was a fear everywhere. Anytime you might be hurt by thugs, anytime the whole bus could turn into ashes..Yes, it was 2015, but our politics might be from stone ages! (Nah, stone age was far more humane!). Each stoppage passed, a fear for next stoppage grabbed our throat.. I was alone that day, but you know, not really..My friend was coming to the puja from a long distant district, another side of the country, only to meet all!

We, the warriors arrived..Loudspeakers, as bugles, welcome us! many other friends, seniors, juniors..We took photos, we ate foods of veneration, yes, we are muslims, but we had a wonderful thought that time. Hindu friends ate as blessings, we ate as foods! We didn’t venerate the statues, but all shared the beauty of it in hearts.

In this world of religious fights, atheism-religion fights, there was a land of fairy tale. Extremists wanted to separate us, but we didn’t separate ourselves! In the year of 2015, we won! My little children, never let this harmony drowned, let mother saraswati’s swan swim…swim across the ocean of unjust, to give us knowledge of right and wrong!

More pictures of Dhaka University, Jagannath Hall Puja, 2014, (as 2015 pictures are not published yet), http://www.somewhereinblog.net/blog/sanjoymukharjeedumb/29923031

Metagenomic virus detection in clinical specimens : a new era

As seen in this Chinese doll picture, the organisms in our nature is not only they look like, they live in an intermingling fashion, which calls for the whole study of them , or the Metagenomics. With the advancement of newer sequencing methods, the area of metagenomics has largely expanded, or on the other way, the broad-range studies of microorganisms in genetic level has geared up the newer and newer inventions of high-throughput sequencing systems. Okay, what it is, Metagenomics is a beautiful study, nothings less important here.

But when we come to the world of viruses, they are not the main ones in the environmental pool. Sure they are present there, but the main sphere of viruses are living cells as they only live well in intracellular condition. In many cases, viruses enter in a body, replicate here, fight with each other or live in peace, spread infections, and when they are shed, from the host body, they are not the same, they have mutated and changed by this time. This made the theory of Quasispecies. So, the environmental study of metagenomics can not be applied here.

Another matter is the studies of Zoonosis. Everyday, there is a new evidence coming out, about, this or that newly emerged disease has come from this or that animals. When a case is found, with no former case, its very difficult to find out the causative agent. So, the specific and effective study of Metagenomics from clinical sample is very important.

This study comes forward with a very new method, tissue-based unbiased virus detection for viral metagenomics (TUViD-VM). Formerly there were many methods available for viral metagenomic study as Hybridization, Sequence independent single primer amplification( SISPA), Arbitrary primed PCR (AP-PCR), Rolling circle amplification etc. This study group from Robert Koch Institute, Germany, not only established a new protocol, but also have shown the efficacy very well.

Schematic description of tissue-based universal virus detection for viral metagenomics protocol. Estimated durations of each step are shown in parentheses. The protocol takes 12 h to complete

This study compared the protocol in different virus groups, different hosts, different extraction, PCR and sequencing methods. The only limitation of this study might be the higher cost for sample processing. It also need high capacity computational analyses as both the viral and host genomes are mixed in a clinical sample gene pool. The researchers nullified the constrain, as sequence data for mammalian hosts are very limited.

This study opened a new era of viral study. Where a newly emerged disease call for an outbreak, and we find nothing in our hands to search the causative agent, as we saw for Ebola just a few days earlier, an established protocol of tissue based viral metagenomics can  help a lot!

Links : http://wwwnc.cdc.gov/eid/article/21/1/14-0766_article

            http://onlinelibrary.wiley.com/doi/10.1002/rmv.532/abstract

also posted at : http://www.sciencenutshell.com/metagenomic-virus-detection-clinical-specimens-new-era/

Next Generation Genome Sequencing – Today And Tommorrow

When Human Genome Project was running, and finally done in 2003, I was in school. The total thing was a sci-fi to me. As they are pouring a drop of blood or a string of hair, and  getting the whole secret story of human written in ATGC ! There were several fun facts published that time, like the distance of sun and earth relative to the length of whole DNA, or the about the mass of it. Sequencing DNA seemed very easy to me until I entered in the Virology lab, where we answer about any unknown thing, like, ahh, do the PCR and sequence it!

In molecular Biology, this thing is common for all organisms, doing PCR and sequencing. The genome is consisted of RNA (only RNA for some viruses) and DNA, but all tends to DNA sequencing, as the RNA is converted into DNA by reverse transcription. DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases—adenine, guanine, cytosine, and thymine—in a strand of DNA.

DNA sequencing is largely done by Sanger sequencing along with Maxam-Gilbert sequencing in some little cases. When we talk about sequencing, we usually refer to the chain termination or Sanger sequencing method. We use this in our lab too, for sequencing several parts of viruses to characterize them. I have never done any whole genome sequence, but some here do it by sequencing part by part and then aligning them.

When I came to know about Metagenomics and Next generation Sequencing that sci-fi feeling came back, but in a polished and I-can-do-it version 🙂 So, I decided to share them with my friends, who may know them already. Here I am skipping the whole thing about Sanger method, just adding a schematic picture to differentiate the two generations.

Figure 1.

http://circgenetics.ahajournals.org/content/6/4/427.figures-only

I collected some stuff from Wikipedia and technique types were from just one source, EMBL-EBI website, as anyone can take the online course at a glance. But there are many other methods, maybe I’ll discuss some if the mood comes back 🙂

Next-generation sequencing (NGS), also known as high-throughput sequencing, is the catch-all term used to describe a number of different modern sequencing technologies, which are given below-

Illumina sequencing

Illumina dye sequencing was based on inventions of S Balasubramanian and D Klenerman of Cambridge University. Here, the slide is flooded with nucleotides and DNA polymerase. These nucleotides are fluorescently labelled, with the colour corresponding to the base. They also have a terminator, so that only one base is added at a time. An image is taken of the slide. In each read location, there will be a fluorescent signal indicating the base that has been added.  The process is repeated, adding one nucleotide at a time and imaging in between. All of the sequence reads will be the same length, as the read length depends on the number of cycles carried out.

http://www.nature.com/nbt/journal/v29/n11/fig_tab/nbt.1996_F1.html

This technique offers a number of advantages over traditional sequencing methods. Due to the automated nature it is possible to sequence multiple strands at once and gain actual sequencing data quickly. Additionally, this method only uses DNA polymerase as opposed to multiple, expensive enzymes required by other sequencing techniques.

454 sequencing

The system relies on fixing nebulized and adapter-ligated DNA fragments to small DNA-capture beads in a water-in-oil emulsion. The DNA fixed to these beads is then amplified by PCR. Each DNA-bound bead is placed into a ~29 μm well on a PicoTiterPlate, a fiber optic chip. A mix of enzymes such as DNA polymerase, ATP sulfurylase, and luciferase are also packed into the well. The PicoTiterPlate is then placed into the GS FLX System for sequencing.

http://www.csulb.edu/~cohlberg/DNAsequencing.html

Ion semiconductor sequencing

Unlike Illumina and 454, Ion torrent and Ion proton sequencing do not make use of optical signals. Instead, they exploit the fact that addition of a dNTP to a DNA polymer releases an H+ ion. Like 454, the slide is flooded with a single species of dNTP, along with buffers and polymerase, one NTP at a time. The pH is detected is each of the wells, as each H+ ion released will decrease the pH. The changes in pH allow us to determine if that base, and how many thereof, was added to the sequence read.

http://dnamismatch.com/dna-sequencing/next-generation-methods/ion-semiconductor-sequencing/

NGS is significantly cheaper, quicker and is more accurate and reliable than Sanger sequencing. It needs least amount of template DNA, as mainly works on the synthesis process, where Sanger methods depends on chain termination. only one read (maximum ~1kb) can be taken at a time in Sanger sequencing, whereas NGS is massively parallel, allowing 300Gb of DNA to be read on a single run on a single chip. It is also useful for shorter and repeated sequences. Today, Next Generation Sequencing are just outside our lab door, and tomorrow we will slide the door and let it in! 😀

also posted at: http://www.sciencenutshell.com/next-generation-genome-sequencing-today-tommorrow/